Frequency-dependent selection in vaccine-associated pneumococcal population dynamics

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Title: Frequency-dependent selection in vaccine-associated pneumococcal population dynamics
Author(s): Corander, J
Fraser, C
Gutmann, MU
Arnold, B
Hanage, WP
Bentley, SD
Lipsitch, M
Croucher, NJ
Item Type: Journal Article
Abstract: Many bacterial species are composed of multiple lineages distinguished by extensive variation in gene content. These often cocirculate in the same habitat, but the evolutionary and ecological processes that shape these complex populations are poorly understood. Addressing these questions is particularly important for Streptococcus pneumoniae, a nasopharyngeal commensal and respiratory pathogen, because the changes in population structure associated with the recent introduction of partial-coverage vaccines have substantially reduced pneumococcal disease. Here we show that pneumococcal lineages from multiple populations each have a distinct combination of intermediate-frequency genes. Functional analysis suggested that these loci may be subject to negative frequency-dependent selection (NFDS) through interactions with other bacteria, hosts or mobile elements. Correspondingly, these genes had similar frequencies in four populations with dissimilar lineage compositions. These frequencies were maintained following substantial alterations in lineage prevalences once vaccination programmes began. Fitting a multilocus NFDS model of post-vaccine population dynamics to three genomic datasets using Approximate Bayesian Computation generated reproducible estimates of the influence of NFDS on pneumococcal evolution, the strength of which varied between loci. Simulations replicated the stable frequency of lineages unperturbed by vaccination, patterns of serotype switching and clonal replacement. This framework highlights how bacterial ecology affects the impact of clinical interventions.Accessory loci are shown to have similar frequencies in diverse Streptococcus pneumoniae populations, suggesting negative frequency-dependent selection drives post-vaccination population restructuring.
Publication Date: 16-Oct-2017
Date of Acceptance: 1-Sep-2017
ISSN: 2397-334X
Publisher: Nature Publishing Group
Start Page: 1950
End Page: 1960
Journal / Book Title: Nature Ecology and Evolution
Volume: 1
Copyright Statement: © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
Sponsor/Funder: Medical Research Council (MRC)
Funder's Grant Number: MR/K010174/1B
Publication Status: Published
Conference Place: England
Appears in Collections:Faculty of Medicine
Epidemiology, Public Health and Primary Care

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